Secrets
by ChocolatyMoonLight
Summary: She knows, she knows all too well who Melody's father is. And she knows who it should be. It should be Rory. The Last Centurion, the boy who waited 2000 years for her. But it isn't. AU. Oneshot. Warning for spoilers ahead. Open to concrit.
1. Chapter 1

A/N: This is my first Doctor Who fanfic, so I'm a little bit sensitive, but I'm more than welcome to any sort of constructive criticism. Obviously this is AU, and in this Melody is not River Song. I'm sort of considering possibly turning this into a chapter fic, but I'm pretty sure it'll probably just say one-shot.

Warnings: Angst, spoilers, and hints at adultery

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><p>Amy Pond gently cradles Melody to her chest, feeling her tiny fingers curl against the chilled skin of her neck. She could stand there for hours, just gently cuddling her daughter, holding her against her chest and whispering sweet words of love and encouragement to her. But she's ever too aware of the multitude of soldiers standing behind her, armed with guns and staring daggers at her. It's like the air is thick with both sorrow and hatred, pity and disgust. Her skin prickles with goose-bumps as the icy air nips at her ravenously.<p>

Amy looks down into her daughter's eyes, her daughter's _green _eyes.

She doesn't have green eyes.

Neither does Rory.

But she knows someone who does.

The Doctor.

The greenest eyes she's ever seen, too, next to Melody's. Crisp, sparkling green, illuminated and twinkling like a maelstrom is raging beneath them. Such a beautiful shade of green. Like grass sparkling with dew in the early morning, turquoise water lapping against a sandy shore.

"Two minutes." The voice of Madam Kovarian is tinged with a sort of sardonic pleasure that makes her chest tighten in pain.

She gently places Melody inside the shocking white crib, sliding her fingers across her pink-tinted skin and committing the feel of it to memory. It's so soft against her skin. Like velvet.

And those eyes.

Those bright, green eyes.

The Doctor's eyes.

She knows, she knows all too well who Melody's father is. And she knows who it should be. It should be Rory. The Last Centurion, the boy who waited 2000 years for her. But it isn't. It isn't Rory's. It could never be Rory's, even though it ought to be. She knows she ought to be as in love with Rory as he is with her, but she isn't. She's known this for such a long time now, and each day she tells herself she will tell him the truth about her feelings for him, but when Rory looks at her with those eyes, so full of unconditional love, she convinces herself she loves him.

"He's the last of his kind." She whispers, feeling a knife trembling in her throat.

Those brilliant green eyes are still staring up at her, and for a brief second she swears she sees the Doctor's face instead of Melody's.

"He looks young, but he's lived for hundreds and hundreds of years." She continues, her eyes now hot with stinging tears.

Melody reaches up at her with her fleshy pink fingers, and they graze against her cheek.

Now tears are rolling down Amy's face. She swallows a ball of pain, choking a little on waterlogged sobs. "And wherever they take you, Melody, however scared you are, I promise you, you will never be alone." She wipes a tear from her face.

Tears dribble down her skin, her face tightens, and pinpricks of pain shoot through her chest. The pain in her throat is so intense she can barely speak now.

"Because this man is your father."

Rory will know. He'll know the minute he sees Melody. He's always been suspicious, always been insecure, and even though it exasperates Amy how angry he gets when she gets close to the Doctor she knows he has every right to be. She doesn't want to imagine how he'll react, but some weird dark part of her can't help but wonder. Will he be angry? Probably. If so, will his anger be at both her and the Doctor? Most definitely.

Amy places a gentle kiss on Melody's forehead. "His name is the Doctor."


	2. Chapter 2

Author's Note: Alright, here's part two. Sorry for the long wait, I was putting it off for a while because I wasn't that sure it'd be good. I'm still feeling a little uncertain, but I think you all have waited long enough, so here you go!

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><p>When the Doctor comes through the door with Melody Pond in his arms, Amy feels her entire body light up with ecstasy. Every nerve, every synapse, every muscle, <em>everything <em>is so awake and so alive. For a brief moment there's a frisson of doubt, and her stomach sinks momentarily with the fear that somehow she's just imagining things, that they're not really there, and that at any second they'll disappear and she'll be alone once more. But as the Doctor gets closer the fear passes and soon she's completely forgotten why she was even scared.

"Doctor!" She cries out, eyes warm with tears of joy.

Amy throws her arms around him and pulls him into a crushing embrace, just barely able to feel his hearts thumping in his chest.

"I knew you'd find us." She whispers in a voice warbled by gleeful sobs.

It seems like they stand there forever, completely removed from the rest of the world. Completely safe, safe from anything and everything. Yet there's also a burgeoning knowledge inside her that their moment of peace is fleeting, as if they're safe inside a box of glass but the glass is paper thin and can be shattered at any moment.

"Here." The Doctor says after slowly pulling back from here.

He gently hands Melody to Amy, and she cradles her against her chest. She looks down at her, and with each passing second she realizes more and more how fragile she is. Even more she realizes how close she had come to losing Melody. If it weren't for the Doctor she might have never seen her daughter again. The thought makes her ache. Then she begins to feel guilt, because she knows that no matter what she does or says to show her thanks to him, it will never fully express her gratitude for all he's done for her.

Melody looks up at her with those brilliant green eyes, and suddenly she feels a sharp pain in her chest. _How do I tell him? _She asks herself, gently rocking her child in her arms.

"She's beautiful." The Doctor says, and Amy swears she sees tears in his eyes. "What's her name?"

"Melody." She replies, now feeling icy and stiff inside.

The Doctor grins, his green eyes sparkling. "Melody Pond. That's a lovely name."

Amy smiles, but the smile falters quickly. She wants to feel happy, she should feel happy, but she can't. Uncertainty tugs at her heartstrings and pain blooms in her chest like a wildfire. _Maybe I just shouldn't tell him. _She wonders. It would be the easiest thing to do. Just don't tell him. But when she looks at him, and she realizes all he must have done to find her and that if it weren't for him Melody would be in the hands of Madame Kovarian, it's painstakingly obvious that he has to know.

"Doctor, have you ever been a father?" She eases into the question casually and smoothly, but inside her body is wracked with fearful tremors and her heart is convulsing frenziedly.

His expression changes when she asks the question. His eyebrows creep together, his lips tighten, and he looks up at her. "Well, sort of once."

"What do you mean?" She says, narrowing her eyes.

"It's hard to explain." He replies, hands shoved in his pockets. "Why do you ask?"

Amy opens her mouth, but she stops to think carefully about what she says next. "Do you remember that night, in the TARDIS?"

That one night, that one night where recklessness, impulsiveness, and stupidity took control, and common sense was thrown out the window. That one night where one simple kiss led to so much more. That one night that had become a source of shame for the both of them, like a wretched scar marring perfect skin. That night that they both pretended to forget.

His expression hardens even more now. "Which night?"

His words are less like a question and more like a realization, and she nods slowly in reply.

"Amelia Pond, what are you getting at?"

Amy looks him in the eyes, which are steely with suspicion, and then the words come tumbling out of her mouth. "Melody is your daughter."


End file.
